Leakage and transport of waste in a waste repository is generally through the circulation of groundwater flow. Waste repository design, therefore, requires the study of the hydraulic performance of the surrounding rock masses in the presence of groundwater. Rock mass permeability, conductivity and flow rate at various depths can be predicted by hydrogeological data of the joint frequency, joint aperture, stress-joint closure relationship and water-table, obtained at shallow subsurface exploration. Predictions using an improved hydraulic model show that the permeability of a rock mass decreases with increasing depth; the groundwater flow into and around the repository, however, increases with repository depth until it reaches a maximum rate. The groundwater flow stabilizes or decreases after the peak rate due to joint closure of the rock mass surrounding the repository under high in situ stress.